Here, we detail a protocol to design and introduce sequence-specific cholesterol-conjugated antisense oligonucleotides into mouse organ culture. We review design principles for "antagomirs", antisense oligos with a cholesterol-moiety modification at the 3', and present an optimized method to apply them onto 3D cultured embryonic pancreas. The method offers an approach to study the developmental functions of individual miRNAs and to evaluate miRNA targets, which is significantly faster and simpler than comparable genetics-based approaches.